diff options
author | 2010-02-11 23:32:28 +0100 | |
---|---|---|
committer | 2010-02-11 23:32:59 +0100 | |
commit | e54a1c3c78a16b35acbeec78a1cc22b697a9359c (patch) | |
tree | 64884f687b28d6837f83b29a148abb761461d3e2 /scripts | |
parent | InCvs (diff) | |
download | sci-e54a1c3c78a16b35acbeec78a1cc22b697a9359c.tar.gz sci-e54a1c3c78a16b35acbeec78a1cc22b697a9359c.tar.bz2 sci-e54a1c3c78a16b35acbeec78a1cc22b697a9359c.zip |
scripts dir cleaned
Diffstat (limited to 'scripts')
-rwxr-xr-x | scripts/portdupe | 36 | ||||
-rw-r--r-- | scripts/stage-blast-db | 41 | ||||
-rw-r--r-- | scripts/update-monomers-db | 48 |
3 files changed, 36 insertions, 89 deletions
diff --git a/scripts/portdupe b/scripts/portdupe new file mode 100755 index 000000000..fd03f8438 --- /dev/null +++ b/scripts/portdupe @@ -0,0 +1,36 @@ +#!/bin/bash +# +# Copyright 2006 David Shakaryan <omp@gentoo.org> +# Distributed under the terms of the GNU General Public License v2 + +PORTDIR="$(portageq envvar PORTDIR)" + +# If an argument is present, use it as the overlay directory. +if [ $1 ]; then + cd ${1} +fi + +# Checking, displaying, etc. +for PACKAGE in */*; do + if [[ -d ${PORTDIR}/${PACKAGE} ]] && [[ $(basename ${PACKAGE}) != "CVS" ]] && grep -q $(dirname ${PACKAGE}) ${PORTDIR}/profiles/categories; then + # Reset versions from last package checked. + PORTPACK_VERS="" + OVERPACK_VERS="" + # Find just package name excluding category. + PACKAGE_BASE="`basename ${PACKAGE}`" + # Find versions of package in portage. + for PORTPACK in `ls ${PORTDIR}/${PACKAGE}/*.ebuild | sed -e 's/.ebuild//'`; do + PORTPACK_VER="`basename ${PORTPACK} | sed s/${PACKAGE_BASE}-//`" + PORTPACK_VERS="${PORTPACK_VERS} ${PORTPACK_VER}" + done + # Find versions of package in overlay. + for OVERPACK in `ls ${PACKAGE}/*.ebuild | sed -e 's/.ebuild//'`; do + OVERPACK_VER="`basename ${OVERPACK} | sed s/${PACKAGE_BASE}-//`" + OVERPACK_VERS="${OVERPACK_VERS} ${OVERPACK_VER}" + done + # Output info with colors. + echo -e "\e[1;33m${PACKAGE}\e[0m" + echo -e " \e[1;35mPortage:\e[0m${PORTPACK_VERS}" + echo -e " \e[1;35mOverlay:\e[0m${OVERPACK_VERS}" + fi +done diff --git a/scripts/stage-blast-db b/scripts/stage-blast-db deleted file mode 100644 index e3722cfee..000000000 --- a/scripts/stage-blast-db +++ /dev/null @@ -1,41 +0,0 @@ -#!/bin/bash - -DATE=$(date "+%Y%m%d") -CHANGE_ENTRY="automatic bump" - -# Find the Documentation dir from sci overlay - -if [[ -f $(basename $0) ]]; then - REPO_DOC=$(pwd) -else - REPO_DOC=$(dirname $0) -fi - - -cd /tmp; -wget http://www.ncbi.nlm.nih.gov/blast/docs/update_blastdb.pl >& /dev/null - -# Ask for which database - -echo "Which db should be updated ?" -echo "" -perl -w update_blastdb.pl --passiv --showall -echo "" -read DB - - -# Fetch the database and rename it - -perl -w update_blastdb.pl --passiv ${DB} - -for mydb in ${DB}*; do - mv ${mydb} ${mydb#.tar.gz}-${DATE}.tar.gz -done - -cd ${REPO_DOC}/../sci-libs/blast-db-${DB}; -git mv blast-db-${DB}*ebuild blast-db-${DB}-${DATE}.ebuild -git add . -echangelog "${CHANGE_ENTRY}" -reapoman -d -v fix -git add . - diff --git a/scripts/update-monomers-db b/scripts/update-monomers-db deleted file mode 100644 index 28e30333c..000000000 --- a/scripts/update-monomers-db +++ /dev/null @@ -1,48 +0,0 @@ -#!/bin/bash - -DATE=$(date "+%y%m%d") -CHANGE_ENTRY="automatic bump" -MIRROR= -TMPDIR="/tmp/${USER}/" - -# Find the Documentation dir from sci overlay - -if [[ -f $(basename $0) ]]; then - REPO_DOC=$(pwd) -else - REPO_DOC=$(dirname $0) -fi - - - -bump_package() { - mv refmac_dictionary.tar.gz monomer-db-0.${DATE}.tar.gz - cp -f monomer-db-0.${DATE}.tar.gz /home/${USER}/science-dist/ -# scp monomer-db-${DATE}.tar.gz ${MIRROR} - - cd ${REPO_DOC}/../sci-libs/monomer-db/ - [[ -f monomer-db-0.${DATE}.ebuild ]] || \ - git mv monomer-db-0.*ebuild monomer-db-0.${DATE}.ebuild - echangelog ${CHANGE_ENTRY} - DISTDIR="${TMPDIR}" repoman -d -v fix - git add . - git ci -m "${CHANGE_ENTRY}" -} - -mkdir ${TMPDIR} -cd ${TMPDIR}; - -wget http://www.ysbl.york.ac.uk/~garib/refmac/data/refmac_dictionary.tar.gz - -SHA_NEW=$(sha256sum refmac_dictionary.tar.gz|awk '{print $1}') -SHA_OLD=$(sed -n -e '/^DIST monomer/p' ${REPO_DOC}/../sci-libs/monomer-db/Manifest | \ - tail -n 1 | awk '{print $9}') - -if [[ ${SHA_OLD} == ${SHA_NEW} ]]; then - echo "Nothing to update" -else - echo "bumping to monomer-db-${DATE} ..." -# bump_package - echo ${SHA_OLD} - echo ${SHA_NEW} -fi |